July 2024
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Current tools are not enough to monitor microscope performance.
FAIR microscope performance monitoring
At MRI we have previously developed a set of Python libraries that, based on previous work [1] will perform that analysis (microscope-metrics) following a well defined schema (microscope-metrics-schema) and manage the input and output data in an OMERO database (microscope-metrics-omero).
This project aims at producing a Python library, named microscopemetrics-dashboard, providing visualization tools to explore the analyzed data.
To the best of our knowledge there are existing software tools [1, 2, 3] that are focused in producing measurements on optical standards to evaluate the performance of the equipment. However these tools are either proprietary or tightly bound to a specific GUI (ImageJ) which limits their implementation with external tools. In this project we want to profit from the great advantages that Python offers to produce a library that integrates well with modern data analysis and management and visualization tools.
We are otherwise strongly basing our work on pre-existing work by the OME consortium and the QUAREP-LiMi and, on the national level, the GT-metrologie of the RT-mfm.
microscopemetrics-dashboard should provide the possibility to implement different interfaces depending on the “access level”, in decreasing order of access privileges:
Core facility staff
Core facility QC processus
Node of National infrastructure
Core facility user
A very simple view for the user. Green-Yellow-Red In the principle it is a good thing to be transparent but difficult to report the general state of the microscope without oversimplifying. A solution might be to provide data without judgement.
Provide a configurable way to provide information. Configurable by the responsible of the core facility. Adding thresholds should be configurable too.
Handle diversity is key.
microscopemetrics-dashboard should provide, and depending on the access level, these visualization posibilities:
Display one set of key metrics over time or given period for:
One single device, including different imaging settings (objective, filter set…).
Multiple devices
Display the state of one particular device and analysis type at a point in time in a very detailed view
Comparing different machines (?).
Other features to discuss and to rank:
The tool will be deployed by the FBI infrastructure for our use case. Docker?
Provide developer and user documentation. Formats to define
Python (Cpython) is the language of choice for developing microscope-metrics and so it will be for microscopemetrics-dashboard. A number of options ara available for developing a dashboard:
A few choices of development tools:
FBI-core facility integration Cedric FBI-data: Guillaume Project responsible: Julio Project developer: Oumou WG-microscope-metrics: WGMM
The development team will meet at least once every three months to discuss about the evolution of the project.
The WGMM will be the initial test group for every release.
Not applicable at this point in time. A 12 month salary has been obtained from FBI.
The estimated human resources available during the length of the project are 12 months full time.
No special environmental conditions are identified.
No special suspensive conditions are identified
Provided by the code testing framework of the software. Yet to identify a test suite to test the GUI.
A test group will be put in place to test the GUI. This group must validate the development.
Milestones to define : 1) finalizing specifications / january 2) writing code and validation / 02-06 3) Carry out unit tests (per measure and per instrument) and integration tests (on one or more instrumental parks of a node) to ensure the proper functioning of the dashboard. 4) Validate compatibility with different OMERO databases within the perimeter of a node. parallelization of the work to design several specificities like metaparameters or custom layout
Code base is stored in GitHub. All other documentation is stored in Taiga. Code related issue tracking is managed in GitHub. Project management is done in Taiga.
The project should be accompanied by documentation for the user and for the developer.
The code is distributed as open source under GPL 3.0. The main reason being that it is the license used by the OME consortium.
All tools are disseminated as open-source GPL3. Available on github.
The public interested in this tool is core facility staff. The tool will be promoted and communicated through the regular routes: meetings, work-groups, presentations,… It is foreseeable to write a paper when a stable version is released.
[1] Cédric Matthews and Fabrice P. Cordelieres, MetroloJ : an ImageJ plugin to help monitor microscopes’ health, in ImageJ User & Developer Conference 2010 proceedings. [2] Theer, P., Mongis, C. & Knop, M. PSFj: know your fluorescence microscope. Nat Methods 11, 981–982 (2014). doi.org/10.1038/nmeth.3102 [3] argolight.com/measure-microscopes-performances-detect-issues-with-daybook [4] https://stackoverflow.blog/2020/05/27/2020-stack-overflow-developer-survey-results/ [5] https://insights.stackoverflow.com/survey/2020